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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for LYVE1 |
Basic gene info. | Gene symbol | LYVE1 |
Gene name | lymphatic vessel endothelial hyaluronan receptor 1 | |
Synonyms | CRSBP-1|HAR|LYVE-1|XLKD1 | |
Cytomap | UCSC genome browser: 11p15 | |
Genomic location | chr11 :10579412-10590365 | |
Type of gene | protein-coding | |
RefGenes | NM_006691.3, | |
Ensembl id | ENSG00000133800 | |
Description | cell surface retention sequence binding protein-1cell surface retention sequence-binding protein 1extracellular link domain containing 1extracellular link domain-containing 1extracellular link domain-containing protein 1hyaluronic acid receptorlymph | |
Modification date | 20141207 | |
dbXrefs | MIM : 605702 | |
HGNC : HGNC | ||
HPRD : 05753 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_LYVE1 | |
BioGPS: 10894 | ||
Gene Expression Atlas: ENSG00000133800 | ||
The Human Protein Atlas: ENSG00000133800 | ||
Pathway | NCI Pathway Interaction Database: LYVE1 | |
KEGG: LYVE1 | ||
REACTOME: LYVE1 | ||
ConsensusPathDB | ||
Pathway Commons: LYVE1 | ||
Metabolism | MetaCyc: LYVE1 | |
HUMANCyc: LYVE1 | ||
Regulation | Ensembl's Regulation: ENSG00000133800 | |
miRBase: chr11 :10,579,412-10,590,365 | ||
TargetScan: NM_006691 | ||
cisRED: ENSG00000133800 | ||
Context | iHOP: LYVE1 | |
cancer metabolism search in PubMed: LYVE1 | ||
UCL Cancer Institute: LYVE1 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for LYVE1(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: LYVE1 |
Familial Cancer Database: LYVE1 |
* This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in |
cf) number; DB name 1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long, 2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/, 3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html, 4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long, 5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php, 1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/ |
Metabolic Pathway Description | |
REACTOME_HYALURONAN_METABOLISM REACTOME_METABOLISM_OF_CARBOHYDRATES |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: LYVE1 |
MedGen: LYVE1 (Human Medical Genetics with Condition) | |
ClinVar: LYVE1 | |
Phenotype | MGI: LYVE1 (International Mouse Phenotyping Consortium) |
PhenomicDB: LYVE1 |
Mutations for LYVE1 |
* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site. |
Structural Variants in COSMIC: go to COSMIC mutation histogram |
There's no structural variation information in COSMIC data for this gene. |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows LYVE1 related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
There's no copy number variation information in COSMIC data for this gene. |
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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=16) | (# total SNVs=4) |
(# total SNVs=0) | (# total SNVs=0) |
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Top 10 SNVs Having the Most Samples in COSMIC data |
* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID. |
GRCh37 position | Mutation(aa) | Unique sampleID count |
chr11:10585563-10585563 | p.G107G | 2 |
chr11:10585602-10585602 | p.F94L | 2 |
chr11:10580685-10580685 | p.T314T | 2 |
chr11:10585864-10585864 | p.A48V | 2 |
chr11:10582129-10582129 | p.F206V | 1 |
chr11:10585591-10585591 | p.S98Y | 1 |
chr11:10582155-10582155 | p.K197I | 1 |
chr11:10582171-10582171 | p.S192A | 1 |
chr11:10585615-10585615 | p.V90G | 1 |
chr11:10580680-10580680 | p.R316Q | 1 |
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SNV Counts per Each Loci in TCGA data |
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Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# sample |   | 1 |   | 3 | 1 |   | 1 |   | 1 |   |   | 3 | 2 |   |   |   | 6 | 3 |   | 1 |
# mutation |   | 1 |   | 3 | 1 |   | 1 |   | 1 |   |   | 3 | 2 |   |   |   | 6 | 3 |   | 1 |
nonsynonymous SNV |   | 1 |   | 3 |   |   | 1 |   | 1 |   |   | 3 | 2 |   |   |   | 3 | 2 |   | 1 |
synonymous SNV |   |   |   |   | 1 |   |   |   |   |   |   |   |   |   |   |   | 3 | 1 |   |   |
cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma]) |
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Top 10 SNVs Having the Most Samples in TCGA data |
* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID. |
Genomic Position | Mutation(aa) | Unique sampleID count |
chr11:10585563 | p.G107G | 2 |
chr11:10585851 | p.E161K | 1 |
chr11:10580759 | p.I140V | 1 |
chr11:10585864 | p.S131L | 1 |
chr11:10582155 | p.L318M | 1 |
chr11:10590003 | p.D72N | 1 |
chr11:10582192 | p.R316Q | 1 |
chr11:10580675 | p.G70D | 1 |
chr11:10582227 | p.T314T | 1 |
chr11:10580680 | p.L52L | 1 |
Other DBs for Point Mutations |
Copy Number for LYVE1 in TCGA |
* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene. |
cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma] |
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Gene Expression for LYVE1 |
Gene Expression in Cancer Cell-lines (CCLE) |
* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
Differential Gene Expression in Primary Tumors (TCGA) |
* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis. (t test, adjusted p<0.05 (using Benjamini-Hochberg FDR)) |
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CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
Co-Expressed gene's network Plot |
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown. Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene |
ABCA6,ABCA8,ABCA9,ANGPTL1,C7,CAV1,CCDC69, CD209,CHST7,CORO2B,HSPB6,LRRN4CL,LYVE1,MMRN1, MRAP,NPR1,NR5A2,PTGIS,STAB2,TCF23,TNXB | BCAT1,CD200R1,CD209,CMKLR1,COLEC12,DAB2,F13A1, FOLR2,FSTL1,GFPT2,GPR1,HPGDS,HRH1,LILRB5, LYVE1,MFAP5,MPEG1,MRC1,RGL1,SCN9A,SLC24A4 |
APLNR,CD93,COL15A1,CXorf36,F13A1,GPR116,HTR2A, IL1R1,LYVE1,NHSL2,NPR1,PREX2,RHOJ,S1PR1, SHE,STARD8,SV2B,TEK,THBD,THSD7A,TIE1 | ABCA6,ABCA9,ADH1B,ALDH1A3,ANXA1,C11orf70,C1S, C7,CDO1,CYP7B1,FMO2,LOC572558,LOH12CR2,LYVE1, NRN1,RBP7,RGL1,SETD7,SNCA,SNCG,TPST1 |
Co-Expressed gene's Protein-protein interaction Network Plot |
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown. Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for LYVE1 |
There's no related Drug. |
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Cross referenced IDs for LYVE1 |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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